Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening
Authors
Keywords
-
Journal
Wiley Interdisciplinary Reviews-Computational Molecular Science
Volume 5, Issue 6, Pages 405-424
Publisher
Wiley
Online
2015-08-28
DOI
10.1002/wcms.1225
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- A Comparative Assessment of Predictive Accuracies of Conventional and Machine Learning Scoring Functions for Protein-Ligand Binding Affinity Prediction
- (2015) Hossam M. Ashtawy et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Deep Neural Nets as a Method for Quantitative Structure–Activity Relationships
- (2015) Junshui Ma et al. Journal of Chemical Information and Modeling
- Improvements, trends, and new ideas in molecular docking: 2012-2013 in review
- (2015) Elizabeth Yuriev et al. JOURNAL OF MOLECULAR RECOGNITION
- Improving AutoDock Vina Using Random Forest: The Growing Accuracy of Binding Affinity Prediction by the Effective Exploitation of Larger Data Sets
- (2015) Hongjian Li et al. Molecular Informatics
- Low-Quality Structural and Interaction Data Improves Binding Affinity Prediction via Random Forest
- (2015) Hongjian Li et al. MOLECULES
- Optimizing the affinity and specificity of ligand binding with the inclusion of solvation effect
- (2015) Zhiqiang Yan et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Polypharmacology modelling using proteochemometrics (PCM): recent methodological developments, applications to target families, and future prospects
- (2015) Isidro Cortés-Ciriano et al. MedChemComm
- Open Drug Discovery Toolkit (ODDT): a new open-source player in the drug discovery field
- (2015) Maciej Wójcikowski et al. Journal of Cheminformatics
- Improved protein–ligand binding affinity prediction by using a curvature-dependent surface-area model
- (2014) Yang Cao et al. BIOINFORMATICS
- Substituting random forest for multiple linear regression improves binding affinity prediction of scoring functions: Cyscore as a case study
- (2014) Hongjian Li et al. BMC BIOINFORMATICS
- Integrating docking scores, interaction profiles and molecular descriptors to improve the accuracy of molecular docking: Toward the discovery of novel Akt1 inhibitors
- (2014) Wenhu Zhan et al. EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY
- Does a More Precise Chemical Description of Protein–Ligand Complexes Lead to More Accurate Prediction of Binding Affinity?
- (2014) Pedro J. Ballester et al. Journal of Chemical Information and Modeling
- Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
- (2014) Yan Li et al. Journal of Chemical Information and Modeling
- Assessment of Machine Learning Reliability Methods for Quantifying the Applicability Domain of QSAR Regression Models
- (2014) Marko Toplak et al. Journal of Chemical Information and Modeling
- A comparative study of family-specific protein–ligand complex affinity prediction based on random forest approach
- (2014) Yu Wang et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Combining Machine Learning Systems and Multiple Docking Simulation Packages to Improve Docking Prediction Reliability for Network Pharmacology
- (2014) Kun-Yi Hsin et al. PLoS One
- istar: A Web Platform for Large-Scale Protein-Ligand Docking
- (2014) Hongjian Li et al. PLoS One
- Machine learning methods in chemoinformatics
- (2014) John B. O. Mitchell Wiley Interdisciplinary Reviews-Computational Molecular Science
- Machine Learning Estimates of Natural Product Conformational Energies
- (2014) Matthias Rupp et al. PLoS Computational Biology
- Chemical, Target, and Bioactive Properties of Allosteric Modulation
- (2014) Gerard J. P. van Westen et al. PLoS Computational Biology
- aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction
- (2013) Douglas E. V. Pires et al. BIOINFORMATICS
- Drug repositioning by structure-based virtual screening
- (2013) Dik-Lung Ma et al. CHEMICAL SOCIETY REVIEWS
- Comparing Neural-Network Scoring Functions and the State of the Art: Applications to Common Library Screening
- (2013) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Computation of Binding Energies Including Their Enthalpy and Entropy Components for Protein–Ligand Complexes Using Support Vector Machines
- (2013) Chaitanya A. K. Koppisetty et al. Journal of Chemical Information and Modeling
- Binding Affinity Prediction for Protein–Ligand Complexes Based on β Contacts and B Factor
- (2013) Qian Liu et al. Journal of Chemical Information and Modeling
- ID-Score: A New Empirical Scoring Function Based on a Comprehensive Set of Descriptors Related to Protein–Ligand Interactions
- (2013) Guo-Bo Li et al. Journal of Chemical Information and Modeling
- SFCscoreRF: A Random Forest-Based Scoring Function for Improved Affinity Prediction of Protein–Ligand Complexes
- (2013) David Zilian et al. Journal of Chemical Information and Modeling
- Consensus Docking: Improving the Reliability of Docking in a Virtual Screening Context
- (2013) Douglas R. Houston et al. Journal of Chemical Information and Modeling
- Water Network Perturbation in Ligand Binding: Adenosine A2A Antagonists as a Case Study
- (2013) Andrea Bortolato et al. Journal of Chemical Information and Modeling
- Using Random Forest To Model the Domain Applicability of Another Random Forest Model
- (2013) Robert P. Sheridan Journal of Chemical Information and Modeling
- Experimental versus predicted affinities for ligand binding to estrogen receptor: iterative selection and rescoring of docked poses systematically improves the correlation
- (2013) James S. Wright et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Optimization of molecular docking scores with support vector rank regression
- (2013) Wei Wang et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Structure-Based Virtual Screening for Drug Discovery: a Problem-Centric Review
- (2012) Tiejun Cheng et al. AAPS Journal
- Machine Learning Techniques and Drug Design
- (2012) J.C. Gertrudes et al. CURRENT MEDICINAL CHEMISTRY
- Machine Learning Methods for Property Prediction in Chemoinformatics: Quo Vadis?
- (2012) Alexandre Varnek et al. Journal of Chemical Information and Modeling
- ZINC: A Free Tool to Discover Chemistry for Biology
- (2012) John J. Irwin et al. Journal of Chemical Information and Modeling
- Characterization of Small Molecule Binding. I. Accurate Identification of Strong Inhibitors in Virtual Screening
- (2012) Bo Ding et al. Journal of Chemical Information and Modeling
- Bioinformatics and variability in drug response: a protein structural perspective
- (2012) J. L. Lahti et al. Journal of the Royal Society Interface
- Hierarchical virtual screening for the discovery of new molecular scaffolds in antibacterial hit identification
- (2012) P. J. Ballester et al. Journal of the Royal Society Interface
- Target-Specific Support Vector Machine Scoring in Structure-Based Virtual Screening: Computational Validation, In Vitro Testing in Kinases, and Effects on Lung Cancer Cell Proliferation
- (2011) Liwei Li et al. Journal of Chemical Information and Modeling
- Support Vector Regression Scoring of Receptor–Ligand Complexes for Rank-Ordering and Virtual Screening of Chemical Libraries
- (2011) Liwei Li et al. Journal of Chemical Information and Modeling
- Comments on “Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets”: Significance for the Validation of Scoring Functions
- (2011) Pedro J. Ballester et al. Journal of Chemical Information and Modeling
- CSAR Benchmark Exercise of 2010: Combined Evaluation Across All Submitted Scoring Functions
- (2011) Richard D. Smith et al. Journal of Chemical Information and Modeling
- A Machine Learning-Based Method To Improve Docking Scoring Functions and Its Application to Drug Repurposing
- (2011) Sarah L. Kinnings et al. Journal of Chemical Information and Modeling
- NNScore 2.0: A Neural-Network Receptor–Ligand Scoring Function
- (2011) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Let’s get honest about sampling
- (2011) David L. Mobley JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
- (2011) Iurii Sushko et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- Discovery of Potent Inhibitors of Soluble Epoxide Hydrolase by Combinatorial Library Design and Structure-Based Virtual Screening
- (2011) Li Xing et al. JOURNAL OF MEDICINAL CHEMISTRY
- BINANA: A novel algorithm for ligand-binding characterization
- (2011) Jacob D. Durrant et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Outstanding challenges in protein-ligand docking and structure-based virtual screening
- (2011) Bohdan Waszkowycz et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- CSCORE: A SIMPLE YET EFFECTIVE SCORING FUNCTION FOR PROTEIN–LIGAND BINDING AFFINITY PREDICTION USING MODIFIED CMAC LEARNING ARCHITECTURE
- (2011) XUCHANG OUYANG et al. Journal of Bioinformatics and Computational Biology
- A machine learning approach to predicting protein–ligand binding affinity with applications to molecular docking
- (2010) Pedro J. Ballester et al. BIOINFORMATICS
- A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval
- (2010) S. J. Swamidass et al. BIOINFORMATICS
- Exploiting PubChem for virtual screening
- (2010) Xiang-Qun Sean Xie Expert Opinion on Drug Discovery
- Ultrafast shape recognition: method and applications
- (2010) Pedro J Ballester Future Medicinal Chemistry
- Binding Affinity Prediction with Property-Encoded Shape Distribution Signatures
- (2010) Sourav Das et al. Journal of Chemical Information and Modeling
- NNScore: A Neural-Network-Based Scoring Function for the Characterization of Protein−Ligand Complexes
- (2010) Jacob D. Durrant et al. Journal of Chemical Information and Modeling
- Leave-Cluster-Out Cross-Validation Is Appropriate for Scoring Functions Derived from Diverse Protein Data Sets
- (2010) Christian Kramer et al. Journal of Chemical Information and Modeling
- Non-additivity of Functional Group Contributions in Protein–Ligand Binding: A Comprehensive Study by Crystallography and Isothermal Titration Calorimetry
- (2010) Bernhard Baum et al. JOURNAL OF MOLECULAR BIOLOGY
- Bioisosteric Replacement and Scaffold Hopping in Lead Generation and Optimization
- (2010) Sarah R. Langdon et al. Molecular Informatics
- Virtual screening: an endless staircase?
- (2010) Gisbert Schneider NATURE REVIEWS DRUG DISCOVERY
- Scoring functions and their evaluation methods for protein–ligand docking: recent advances and future directions
- (2010) Sheng-You Huang et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Efficient Drug Lead Discovery and Optimization
- (2009) William L. Jorgensen ACCOUNTS OF CHEMICAL RESEARCH
- A statistical framework to evaluate virtual screening
- (2009) Wei Zhao et al. BMC BIOINFORMATICS
- Computational Intelligence Methods for Docking Scores
- (2009) David Hecht et al. Current Computer-Aided Drug Design
- Computational evaluation of protein–small molecule binding
- (2009) Olgun Guvench et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Mining free compound databases to identify candidates selected by virtual screening
- (2009) Sridhar R Vasudevan et al. Expert Opinion on Drug Discovery
- Comparative Assessment of Scoring Functions on a Diverse Test Set
- (2009) Tiejun Cheng et al. Journal of Chemical Information and Modeling
- Maximum Unbiased Validation (MUV) Data Sets for Virtual Screening Based on PubChem Bioactivity Data
- (2009) Sebastian G. Rohrer et al. Journal of Chemical Information and Modeling
- Predicting the Predictability: A Unified Approach to the Applicability Domain Problem of QSAR Models
- (2009) Horvath Dragos et al. Journal of Chemical Information and Modeling
- Combining Machine Learning and Pharmacophore-Based Interaction Fingerprint for in Silico Screening
- (2009) Tomohiro Sato et al. Journal of Chemical Information and Modeling
- AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
- (2009) Garrett M. Morris et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Distance Dependent Scoring Function for Describing Protein−Ligand Intermolecular Interactions
- (2008) Natalia Artemenko Journal of Chemical Information and Modeling
- SFCscore: Scoring functions for affinity prediction of protein-ligand complexes
- (2008) Christoph A. Sotriffer et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreAdd your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload Now